1
|
Roberts MG, Dent MR, Ramos S, Thielges MC, Burstyn JN. Probing conformational dynamics of DNA binding by CO-sensing transcription factor, CooA. J Inorg Biochem 2024; 259:112656. [PMID: 38986290 DOI: 10.1016/j.jinorgbio.2024.112656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/29/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
The transcription factor CooA is a CRP/FNR (cAMP receptor protein/ fumarate and nitrate reductase) superfamily protein that uses heme to sense carbon monoxide (CO). Allosteric activation of CooA in response to CO binding is currently described as a series of discrete structural changes, without much consideration for the potential role of protein dynamics in the process of DNA binding. This work uses site-directed spin-label electron paramagnetic resonance spectroscopy (SDSL-EPR) to probe slow timescale (μs-ms) conformational dynamics of CooA with a redox-stable nitroxide spin label, and IR spectroscopy to probe the environment at the CO-bound heme. A series of cysteine substitution variants were created to selectively label CooA in key functional regions, the heme-binding domain, the 4/5-loop, the hinge region, and the DNA binding domain. The EPR spectra of labeled CooA variants are compared across three functional states: Fe(III) "locked off", Fe(II)-CO "on", and Fe(II)-CO bound to DNA. We observe changes in the multicomponent EPR spectra at each location; most notably in the hinge region and DNA binding domain, broadening the description of the CooA allosteric mechanism to include the role of protein dynamics in DNA binding. DNA-dependent changes in IR vibrational frequency and band broadening further suggest that there is conformational heterogeneity in the active WT protein and that DNA binding alters the environment of the heme-bound CO.
Collapse
Affiliation(s)
- Madeleine G Roberts
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, United States
| | - Matthew R Dent
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, United States
| | - Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Judith N Burstyn
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, United States.
| |
Collapse
|
2
|
Aono S, Nakajima H. Transcriptional Regulation of Gene Expression by Metalloproteins. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967400103165128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
FNR and SoxR are transcriptional regulators containing an iron–sulfur cluster. The iron–sulfur cluster in FNR acts as an oxygen sensor by reacting with oxygen. The structural change of the iron–sulfur cluster takes place when FNR senses oxygen, which regulates the transcriptional regulator activity of FNR through the change of the quaternary structure. SoxR contains the [2Fe–2S] cluster that regulates the transcriptional activator activity of SoxR. Only the oxidized SoxR containing the [2Fe–2S]2+ cluster is active as the transcriptional activator. CooA is a transcriptional activator containing a protoheme that acts as a CO sensor. CO is a physiological effector of CooA and regulates the transcriptional activator activity of CooA. In this review, the biochemical and biophysical properties of FNR, SoxR, and CooA are described.
Collapse
Affiliation(s)
- Shigetoshi Aono
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
| | - Hiroshi Nakajima
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
| |
Collapse
|
3
|
Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, C Gomes AL, Galagan JE, McDonough KA. Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res 2015; 44:134-51. [PMID: 26358810 PMCID: PMC4705688 DOI: 10.1093/nar/gkv889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/26/2015] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ∼200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.
Collapse
Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Anna Lyubetskaya
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Gwendowlyn S Knapp
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | | | - Michaela Gazdik
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | | | - James E Galagan
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| |
Collapse
|
4
|
Abstract
The haem-based sensors are chimeric multi-domain proteins responsible for the cellular adaptive responses to environmental changes. The signal transduction is mediated by the sensing capability of the haem-binding domain, which transmits a usable signal to the cognate transmitter domain, responsible for providing the adequate answer. Four major families of haem-based sensors can be recognized, depending on the nature of the haem-binding domain: (i) the haem-binding PAS domain, (ii) the CO-sensitive carbon monoxide oxidation activator, (iii) the haem NO-binding domain, and (iv) the globin-coupled sensors. The functional classification of the haem-binding sensors is based on the activity of the transmitter domain and, traditionally, comprises: (i) sensors with aerotactic function; (ii) sensors with gene-regulating function; and (iii) sensors with unknown function. We have implemented this classification with newly identified proteins, that is, the Streptomyces avermitilis and Frankia sp. that present a C-terminal-truncated globin fused to an N-terminal cofactor-free monooxygenase, the structural-related class of non-haem globins in Bacillus subtilis, Moorella thermoacetica, and Bacillus anthracis, and a haemerythrin-coupled diguanylate cyclase in Vibrio cholerae. This review summarizes the structures, the functions, and the structure-function relationships known to date on this broad protein family. We also propose unresolved questions and new possible research approaches.
Collapse
|
5
|
Ishida T, Aono S. A model theoretical study on ligand exchange reactions of CooA. Phys Chem Chem Phys 2013; 15:6139-48. [DOI: 10.1039/c3cp43253j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
6
|
Zacharia VM, Shiloh MU. Effect of carbon monoxide on Mycobacterium tuberculosis pathogenesis. Med Gas Res 2012; 2:30. [PMID: 23244630 PMCID: PMC3537638 DOI: 10.1186/2045-9912-2-30] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/04/2012] [Indexed: 12/19/2022] Open
Abstract
The intracellular pathogen Mycobacterium tuberculosis (Mtb) is exposed to multiple host antimicrobial pathways, including toxic gases such as superoxide, nitric oxide and carbon monoxide (CO). To survive, mycobacteria evolved mechanisms to resist the toxic environment, and in this review we focus on a relatively new field, namely, the role of macrophage heme oxygenase and its enzymatic product CO in Mtb pathogenesis. In particular, we focus on (i) the induction of heme oxygenase during Mtb infection and its relevance to Mtb pathogenesis, (ii) the ability of mycobacteria to catabolize CO, (iii) the transcriptional reprogramming of Mtb by exposure to CO, (iv) the general antimicrobial properties of CO and (v) new genetic evidence characterizing the ability of Mtb to resist CO toxicity. Developing a complete molecular and genetic understanding of the pathogenesis of Mtb is essential to its eventual eradication.
Collapse
Affiliation(s)
- Vineetha M Zacharia
- Department of Microbiology, Division of Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75229-9113, USA.
| | | |
Collapse
|
7
|
Lee AJ, Clark RW, Youn H, Ponter S, Burstyn JN. Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA. Biochemistry 2009; 48:6585-97. [PMID: 19594171 DOI: 10.1021/bi801827j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CooA is a heme-dependent CO-sensing transcription factor that has three observable heme coordination states. There is some evidence that each CooA heme state has a distinct protein conformation; the goal of this study was to characterize these conformations by measuring their structural stabilities through guanidine hydrochloride (GuHCl) denaturation. By studying the denaturation processes of the Fe(III) state of WT CooA and several variants, we were able to characterize independent unfolding processes for each domain of CooA. This information was used to compare the unfolding profiles of various CooA heme activation states [Fe(III), Fe(II), and Fe(II)-CO] to show that the heme coordination state changes the stability of the effector binding domain. A mechanism consistent with the data predicts that all CooA coordination states and variants undergo unfolding of the DNA-binding domain between 2 and 3 M GuHCl with a free energy of unfolding of approximately 17 kJ/mol, while unfolding of the heme domain is variable and dependent on the heme coordination state. The findings support a model in which changes in heme ligation alter the structural stability of the heme domain and dimer interface but do not alter the stability of the DNA-binding domain. These studies provide evidence that the domains of transcription factors are modular and that allosteric signaling occurs through changes in the relative positions of the protein domains without affecting the structure of the DNA-binding region.
Collapse
Affiliation(s)
- Andrea J Lee
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | | | | | | |
Collapse
|
8
|
Abstract
Diatomic gas molecules such as O2, CO and NO act as signaling molecules in many biological systems, where metal-containing gas sensor proteins sense their effector gas molecules by using prosthetic groups such as heme, iron-sulfur clusters and non-heme iron as the active center for gas sensing. When the gas sensor proteins sense their effector gas molecules, intramolecular and intermolecular signal transductions take place to regulate many physiological functions including gene expression, aerotaxis, and change in metabolic pathways, etc. The metal-containing prosthetic groups in these sensor proteins play a crucial role for selective sensing of their effectors. In this perspective, I will discuss the structure and function of some O2-, CO- and NO-sensor proteins, especially focussing on the structural, biochemical and biophysical properties of the active centers of these sensor proteins.
Collapse
Affiliation(s)
- Shigetoshi Aono
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Japan.
| |
Collapse
|
9
|
Komori H, Inagaki S, Yoshioka S, Aono S, Higuchi Y. Crystal Structure of CO-sensing Transcription Activator CooA Bound to Exogenous Ligand Imidazole. J Mol Biol 2007; 367:864-71. [PMID: 17292914 DOI: 10.1016/j.jmb.2007.01.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Revised: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
CooA is a CO-dependent transcriptional activator and transmits a CO-sensing signal to a DNA promoter that controls the expression of the genes responsible for CO metabolism. CooA contains a b-type heme as the active site for sensing CO. CO binding to the heme induces a conformational change that switches CooA from an inactive to an active DNA-binding form. Here, we report the crystal structure of an imidazole-bound form of CooA from Carboxydothermus hydrogenoformans (Ch-CooA). In the resting form, Ch-CooA has a six-coordinate ferrous heme with two endogenous axial ligands, the alpha-amino group of the N-terminal amino acid and a histidine residue. The N-terminal amino group of CooA that is coordinated to the heme iron is replaced by CO. This substitution presumably triggers a structural change leading to the active form. The crystal structure of Ch-CooA reveals that imidazole binds to the heme, which replaces the N terminus, as does CO. The dissociated N terminus is positioned approximately 16 A from the heme iron in the imidazole-bound form. In addition, the heme plane is rotated by 30 degrees about the normal of the porphyrin ring compared to that found in the inactive form of Rhodospirillum rubrum CooA. Even though the ligand exchange, imidazole-bound Ch-CooA remains in the inactive form for DNA binding. These results indicate that the release of the N terminus resulting from imidazole binding is not sufficient to activate CooA. The structure provides new insights into the structural changes required to achieve activation.
Collapse
Affiliation(s)
- Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | | | | | | | | |
Collapse
|
10
|
Yamashita T, Hoashi Y, Tomisugi Y, Ishikawa Y, Uno T. The C-helix in CooA Rolls upon CO Binding to Ferrous Heme. J Biol Chem 2004; 279:47320-5. [PMID: 15326178 DOI: 10.1074/jbc.m407766200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA is a homodimeric transcriptional activator from Rhodospirillum rubrum containing one heme in each subunit. CO binding to the heme in its sensor domain activates CooA, facilitating the binding to DNA by its DNA-binding domain. The C-helix links the two domains and shapes an interface between the subunits. To probe the nature of CO activation, residues at positions 112-121 on the C-helix were replaced by Asn or Gln and their effects were evaluated by resonance Raman spectroscopy and by the measurements of CO binding affinity. The nu(Fe-CO) stretching Raman line in CO-bound wild-type CooA was up-shifted by 6 cm(-1) in the L116Q, G117N, and L120Q mutants, indicating unequivocally that these residues are close to the bound CO. Residues Leu116 and Leu120 from each subunit form contacts with the corresponding residues in the opposite subunit, enabling hydrophobic interactions in the inactive ferrous form. Thus, in the CO-bound activated form, both C-helices appear to roll to direct these residues toward the heme, forming a hydrophobic pocket for the bound CO. The CO affinity is approximately one order of magnitude higher in the L112Q, I115Q, L116Q, G117N, L120Q, and T121N mutants but reduced in A114N mutant. The variation indicates that these residues are close to the heme in the ferrous and/or CO-bound forms and are responsible for CooA activation. A roll-and-slide mechanism is proposed for CO activation of CooA.
Collapse
Affiliation(s)
- Taku Yamashita
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oehonmachi, Kumamoto 862-0973, Japan
| | | | | | | | | |
Collapse
|
11
|
Akiyama S, Fujisawa T, Ishimori K, Morishima I, Aono S. Activation mechanisms of transcriptional regulator CooA revealed by small-angle X-ray scattering. J Mol Biol 2004; 341:651-68. [PMID: 15288777 DOI: 10.1016/j.jmb.2004.06.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Revised: 06/03/2004] [Accepted: 06/07/2004] [Indexed: 10/26/2022]
Abstract
CooA, a heme-containing transcriptional activator, binds CO to the heme moiety and then undergoes a structural change that promotes the specific binding to the target DNA. To elucidate the activation mechanism coupled to CO binding, we investigated the CO-dependent structural transition of CooA with small-angle X-ray scattering (SAXS). In the absence of CO, the radius of gyration Rg and the second virial coefficient (A2) were 25.3(+/-0.5)A and -0.39(+/-0.25) x 10(-4)ml mol g(-2), respectively. CO binding caused a slight increase in Rg (by 0.5A) and a marked decrease in A2 (by 5.09 x 10(-4)ml mol g(-2)). The observed decrease in A2 points to higher attractive interactions between CO-bound CooA molecules in solution compared with CO-free CooA. Although the minor alternation of Rg rules out changes in the overall structure, the marked change in the surface properties points to a CO-induced conformational transition. The experimental Rg and SAXS curves of the two states did not agree with the crystal structure of CO-free CooA. We thus simulated the solution structures of CooA based on the experimental data using rigid-body refinements as well as low-resolution model reconstructions. Both results demonstrate that the hinge region connecting the N-terminal heme domain and C-terminal DNA-binding domain is kinked in CO-free CooA, so that the two domains are positioned close to each other. The CO-dependent structural change observed by SAXS corresponds to a slight swing of the DNA-binding domains away from the heme domains coupled with their rotation by about 8 degrees around the axis of 2-fold symmetry.
Collapse
Affiliation(s)
- Shuji Akiyama
- RIKEN Harima Institute/SPring-8, Structural Biochemistry Laboratory, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan
| | | | | | | | | |
Collapse
|
12
|
Aono S. Biochemical and biophysical properties of the CO-sensing transcriptional activator CooA. Acc Chem Res 2003; 36:825-31. [PMID: 14622029 DOI: 10.1021/ar020097p] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of heme-containing gas sensor proteins have revealed a novel function for heme, which acts as an active site for sensing the corresponding gas molecule of a physiological effector. Heme-based O(2), NO, and CO sensor proteins have now been described in which these gas molecules act as a signaling factor that regulates the functional activity of the sensor proteins. CooA is a CO-sensing transcriptional activator found in the photosynthetic bacterium Rhodospirillum rubrum. The binding of CO to the heme group stimulates the transcriptional activator activity of CooA. The mechanisms of CO sensing by CooA and CO-dependent activation of CooA have now been analyzed by both molecular biological and spectroscopic studies and are discussed in this Account.
Collapse
Affiliation(s)
- Shigetoshi Aono
- Center for Integrative Bioscience, Okazaki National Research Institutes, 38 Nishigo-naka, Myodaiji, Okazaki 444-8585, Japan
| |
Collapse
|
13
|
Kerby RL, Youn H, Thorsteinsson MV, Roberts GP. Repositioning about the dimer interface of the transcription regulator CooA: a major signal transduction pathway between the effector and DNA-binding domains. J Mol Biol 2003; 325:809-23. [PMID: 12507482 DOI: 10.1016/s0022-2836(02)01203-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Activation of the homodimeric transcriptional regulator CooA depends on the coupling of CO binding at an effector domain heme with the allosteric repositioning of the DNA-binding domain F-helix that promotes specific DNA interaction. By analogy to the homologous cAMP receptor protein (CRP), it has been proposed that effector binding elicits subunit reorientation about their coiled-coil C-helix interface, and that this effector domain reorientation stabilizes the active position of the DNA-binding domains. Here, we describe experiments in which effector-independent "CooA*" variants were selected following randomization of a six-residue portion of the C-helix dimerization domain. Subsequent activity analyses, both in vivo and in vitro, were consistent with a model wherein improved C-helix "leucine zipper" interactions modestly shifted the regulator population equilibrium towards the active conformation, although full activation remained CO-dependent. However, in addition to the improved leucine zipper, maximal CooA* activity required additional C-helix changes which in a WT background decreased normal CO-dependent DNA-binding 100-fold. This seemingly paradoxical combination suggested that maximal CooA* activity depended both on the improved coiled-coil interactions and the decoupling of the signal pathway within the effector domain. Both types of C-helix changes indicate that its repositioning is crucial for the allosteric shift in the inactive/active equilibrium of the DNA-binding domain.
Collapse
Affiliation(s)
- Robert L Kerby
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, 106 E. B. Fred Hall, Madison, WI 53706, USA
| | | | | | | |
Collapse
|
14
|
Nakajima H, Nakagawa E, Kobayashi K, Tagawa S, Aono S. Ligand-switching intermediates for the CO-sensing transcriptional activator CooA measured by pulse radiolysis. J Biol Chem 2001; 276:37895-9. [PMID: 11487580 DOI: 10.1074/jbc.m105429200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CooA is a heme-containing and CO-sensing transcriptional activator whose activity is regulated by CO. The protoheme that acts as a CO sensor in CooA shows unique properties for its coordination structure. The Cys75 axial ligand of the ferric heme is replaced by His77 upon the reduction of the heme iron and vice versa. In this work, the ligand-switching process induced by the reduction of the heme was investigated by the technique of pulse radiolysis. Hydrated electron reduced the heme iron in ferric CooA within 1 micros to form the first intermediate with the Soret peak at 440 nm, suggesting that a six-coordinate ferrous heme with a thiolate axial ligand was formed initially. The first intermediate was converted into the second intermediate with the time constant of 40 micros (k = 2.5 x 10(4) x s(-1)). In the second intermediate, the thiolate from Cys75 was thought to be protonated and/or the Fe-S bond was thought to be elongated. The second intermediate was converted into the final reduced form with the time constant of 2.9 ms (k = 3.5 x 10(2) x s(-1)) for wild-type CooA. The ligand exchange between Cys75 and His77 took place during the conversion of the second intermediate into the final reduced form.
Collapse
Affiliation(s)
- H Nakajima
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Nomi-gun, Ishikawa 923-1292, Japan
| | | | | | | | | |
Collapse
|
15
|
Aono S, Honma Y, Ohkubo K, Tawara T, Kamiya T, Nakajima H. CO sensing and regulation of gene expression by the transcriptional activator CooA. J Inorg Biochem 2000; 82:51-6. [PMID: 11132638 DOI: 10.1016/s0162-0134(00)00139-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transcriptional activator CooA from Rhodospirillum rubrum contains a six-coordinate protoheme that acts as a CO sensor in vivo. CO is a physiological effector of CooA and replaces one of the axial ligands of the ferrous heme to form the CO-bound CooA that is active as the transcriptional activator. Cys75 or His77 is coordinated to the ferric and ferrous hemes in CooA, respectively. The redox-controlled ligand exchange between Cys75 and His77 proceeds during the change in the redox state of the heme. The reduction and oxidation midpoint potentials of CooA have been determined to be -320 and -260 mV, respectively. The properties of a functional chimera derived from CRP and CooA suggest that CooA activates the transcription by a similar mechanism to that for CRP at Class II CRP-dependent promoters. Alanine-scanning mutagenesis has revealed that Arg24 and Arg53 of CooA, which will be concerned with the protein-protein interaction with RNA polymerase, are critical amino acid residues for the transcriptional activator activity of CooA, and that Lys26 and Asp94 modulate the activity of CooA.
Collapse
Affiliation(s)
- S Aono
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi-gun, Ishikawa.
| | | | | | | | | | | |
Collapse
|
16
|
Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol 2000; 301:415-31. [PMID: 10926518 DOI: 10.1006/jmbi.2000.3954] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.
Collapse
Affiliation(s)
- H Miyatake
- RIKEN Harima Institute/SPring-8, 1-1-1 Koto, Hyogo, Mikazuki-cho, 679-5148, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Nakajima H, Matsuo T, Tawara T, Aono S. Control of CooA activity by the mutation at the C-terminal end of the heme-binding domain. J Inorg Biochem 2000; 78:63-8. [PMID: 10714706 DOI: 10.1016/s0162-0134(99)00210-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A constitutively active mutant of a CooA, in which Met131 was replaced by Leu, was isolated by random mutagenesis. Site-directed mutagenesis at position 131 revealed that M131R-CooA was also constitutively active even in the absence of CO and that M131P-, M131D-, and M131E-CooA were constitutively inactive regardless of the presence or absence of CO. While M131L- and M131E-CooA showed almost the same electronic absorption spectra as those of the wild type in the ferric, ferrous, and CO-bound forms, M131D-CooA showed the typical spectrum of a five-coordinate heme protein in the ferric form. The conformational change around the heme induced by CO binding, which triggers the activation of CooA, is thought to be linked to the rearrangement of the conformation around the hinge region between the heme-binding and DNA-binding domains and/or of the relative orientation of the two domains to activate CooA.
Collapse
Affiliation(s)
- H Nakajima
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi-gun, Ishikawa
| | | | | | | |
Collapse
|